Keyword search (4,164 papers available)

"Orabi EA" Authored Publications:

Title Authors PubMed ID
1 Modeling CH sub 3 /sub SOH-aromatic complexes to probe cysteine sulfenic acid-aromatic interactions in proteins Orabi EA; English AM; 40994121
CHEMBIOCHEM
2 Modeling predicts facile release of nitrite but not nitric oxide from the thionitrate CH3SNO2 with relevance to nitroglycerin bioactivation Parmar V; Orabi EA; English AM; Peslherbe GH; 39738238
CERMM
3 Ammonium transporters achieve charge transfer by fragmenting their substrate Wang S; Orabi EA; Baday S; Bernèche S; Lamoureux G; 22631217
CERMM
4 New Megastigmane and Polyphenolic Components of Henna Leaves and Their Tumor-Specific Cytotoxicity on Human Oral Squamous Carcinoma Cell Lines Orabi MAA; Orabi EA; Awadh AAA; Alshahrani MM; Abdel-Wahab BA; Sakagami H; Hatano T; 38001804
CHEMBIOCHEM
5 Structural determination and anticholinesterase assay of C-glycosidic ellagitannins from Lawsonia inermis leaves: A study supported by DFT calculations and molecular docking Orabi MAA; Orabi EA; Abdel-Sattar ES; English AM; Hatano T; Elimam H; 36423882
CHEMBIOCHEM
6 Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H2O2 and H2O Orabi EA; English AM; 33356279
CHEMBIOCHEM
7 Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains Orabi EA; Davis RL; Lamoureux G; 31652004
CERMM
8 Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations Orabi EA; Peslherbe GH; 31297500
CHEMBIOCHEM
9 Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone Orabi EA; English AM; 31214677
CHEMBIOCHEM
10 Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone Orabi EA; English AM; 30168822
CHEMBIOCHEM

 

Title:Modeling CH sub 3 /sub SOH-aromatic complexes to probe cysteine sulfenic acid-aromatic interactions in proteins
Authors:Orabi EAEnglish AM
Link:https://pubmed.ncbi.nlm.nih.gov/40994121/
DOI:10.1039/d5cp02976g
Publication:Physical chemistry chemical physics : PCCP
Keywords:
PMID:40994121 Category: Date Added:2025-09-25
Dept Affiliation: CHEMBIOCHEM
1 Center for Research in Molecular Modeling (CERMM), Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada. ann.english@concordia.ca.
2 Current address: Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.

Description:

Cysteine sulfenic acid (CysOH), formed on oxidation of Cys residues, is an intermediate in the catalytic cycles of numerous antioxidant enzymes and participates in oxidative-stress sensing and redox signaling. Proteins control CysOH reactivity in part by its interactions with aromatic residues. To characterize such interactions, we performed extensive ab initio quantum mechanical calculations with MP2(full)/6-311++G(d,p) on complexes of CH3SOH as a CysOH model with side-chain models for Phe (toluene), Trp (3-methylindole), Tyr/Tyr- (4-methylphenol/4-methylphenolate) and His/HisH+ (4-methylimidazole/4-methylimidazolium) residues. The gas-phase global minima conformers extracted from the 67 aromatic complexes found exhibit binding energies of ~-5 to -25 kcal mol-1. In the neutral CH3SOH-aromatics, the center oxidized is the stronger H-bond donor, which varies with the geometry of the complex as does the ionization potential (IPV). While CH3SOH (IPV = 9.20 eV) is exclusively oxidized when complexed to 4-methylimidazolium (IPV = 14.64 eV), the phenol ring is oxidized in all CH3SOH complexes with 4-methylphenolate (IPV = 3.31 eV). To perform molecular dynamics (MD) simulations of the aqueous complexes, a potential model was optimized for CH3SOH and calibrated for its interactions with the aromatic ions. The MD simulations reveal that in bulk water the S atom preferentially adopts en-face or intermediate binding geometry with binding free energies of ~-0.6, -2.5 and -5 kcal mol-1 for the neutral, imidazolium and phenolate complexes, respectively. Overall, the gas-phase and aqueous CH3SOH complexes are 40-170% more stable and 0-40% less stable, respectively, than their CH3SH counterparts. Exceptionally, aqueous 4-methylphenolate binds CH3SOH ~50% more tightly than CH3SH due to strong s-type O-H?Oar H-bond bonding. Examination of a subset of CysOH-aromatics from the Protein Data Bank highlight their role in CysOH formation and stabilization in proteins.





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